A comprehensive review of non-coding RNAs functions in multiple sclerosis

Ghafouri‐Fard, Soudeh; Taheri, Mohammad

doi:10.1016/j.ejphar.2020.173127

Cited by 25 publications

(18 citation statements)

References 36 publications

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“…All of the continuously accumulating data suggest that various non-coding RNA species and the so-called "competing endogenous RNA network” (the detailed reporting of which is unfortunately well beyond the scope of this article, for very extensive literature and a review on the matter see [ 446 , 447 , 448 , 449 ]) might contribute to MS pathogenesis via several already known and yet to be discovered pathways and mechanisms. Circular RNAs are prominent members of this family onto whom intense research has been focused in recent years.…”

Section: Fluid Biomarkers Of Multiple Sclerosismentioning

confidence: 99%

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: A Focus on Neurofilaments and Therapeutic Considerations

Biernacki

Kokas

Sandi

et al. 2022

IJMS

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Introduction: Multiple Sclerosis (MS) is the most common immune-mediated chronic neurodegenerative disease of the central nervous system (CNS) affecting young people. This is due to the permanent disability, cognitive impairment, and the enormous detrimental impact MS can exert on a patient’s health-related quality of life. It is of great importance to recognise it in time and commence adequate treatment at an early stage. The currently used disease-modifying therapies (DMT) aim to reduce disease activity and thus halt disability development, which in current clinical practice are monitored by clinical and imaging parameters but not by biomarkers found in blood and/or the cerebrospinal fluid (CSF). Both clinical and radiological measures routinely used to monitor disease activity lack information on the fundamental pathophysiological features and mechanisms of MS. Furthermore, they lag behind the disease process itself. By the time a clinical relapse becomes evident or a new lesion appears on the MRI scan, potentially irreversible damage has already occurred in the CNS. In recent years, several biomarkers that previously have been linked to other neurological and immunological diseases have received increased attention in MS. Additionally, other novel, potential biomarkers with prognostic and diagnostic properties have been detected in the CSF and blood of MS patients. Areas covered: In this review, we summarise the most up-to-date knowledge and research conducted on the already known and most promising new biomarker candidates found in the CSF and blood of MS patients. Discussion: the current diagnostic criteria of MS relies on three pillars: MRI imaging, clinical events, and the presence of oligoclonal bands in the CSF (which was reinstated into the diagnostic criteria by the most recent revision). Even though the most recent McDonald criteria made the diagnosis of MS faster than the prior iteration, it is still not an infallible diagnostic toolset, especially at the very early stage of the clinically isolated syndrome. Together with the gold standard MRI and clinical measures, ancillary blood and CSF biomarkers may not just improve diagnostic accuracy and speed but very well may become agents to monitor therapeutic efficacy and make even more personalised treatment in MS a reality in the near future. The major disadvantage of these biomarkers in the past has been the need to obtain CSF to measure them. However, the recent advances in extremely sensitive immunoassays made their measurement possible from peripheral blood even when present only in minuscule concentrations. This should mark the beginning of a new biomarker research and utilisation era in MS.

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Section: Fluid Biomarkers Of Multiple Sclerosismentioning

confidence: 99%

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: A Focus on Neurofilaments and Therapeutic Considerations

Biernacki

Kokas

Sandi

et al. 2022

IJMS

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show abstract

“…All of the continuously accumulating data suggest that various non-coding RNA species and the so-called "competing endogenous RNA network" (the detailed reporting of which is unfortunately well beyond the scope of this article, for very extensive literature and a review on the matter see [451][452][453][454] ) might contribute to MS pathogenesis via several already known and yet to be discovered pathways and mechanisms. Circular RNAs are prominent members of this family onto whom intense research has been focused in recent years.…”

Section: Neurofilament Heavy Chain In Msmentioning

confidence: 99%

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: a Comprehensive Review of the Literature with a Focus on Neurofilaments and Therapeutic Considerations

Biernacki¹,

Kokas²,

Sandi³

et al. 2022

Preprint

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Introduction: multiple sclerosis (MS) is the most common immune-mediated chronic neurodegenerative disease of the central nervous system (CNS), affecting young people. Due to the permanent disability, cognitive impairment, and the enormous detrimental impact MS can exert on the patients’ health-related quality of life. It is of great importance to recognise it in time and commence adequate treatment at an early stage. The currently used disease-modifying therapies (DMT) aim to reduce disease activity and thus halt disability development, which in current clinical practice are monitored by clinical and imaging parameters but not by biomarkers found in blood and/or the cerebrospinal fluid (CSF). Both clinical and radiological measures routinely used to monitor disease activity lack information on the fundamental pathophysiological features and mechanisms of MS. Furthermore, they lag behind the disease process itself. By the time a clinical relapse becomes evident or a new lesion appears on the MRI scan, potentially irreversible damage has already occurred in the CNS. In recent years several biomarkers that previously have been linked to other neurological and immunological diseases have received increased attention in MS. Additionally, other novel, potential biomarkers with prognostic and diagnostic properties have been detected in the CSF and blood of MS patients. Areas covered: in this review, we summarise the most up to date knowledge and research conducted on the already known and most promising new biomarker candidates found in the CSF and blood of MS patients. Author commentary: the current diagnostic criteria of MS rely on three pillars; MRI imaging, clinical events and the presence of oligoclonal bands in the CSF (which was reinstated into the diagnostic criteria by the most recent revision). Even though the most recent McDonald criteria made the diagnosis of MS faster than the prior iteration, it is still not an infallible diagnostic toolset, especially at the very early stage of clinically isolated syndrome. Together with the gold standard MRI and clinical measures, ancillary blood and CSF biomarkers may not just improve diagnostic accuracy and speed but very well may become agents to monitor therapeutic efficacy and make even more personalised treatment in MS a reality in the near future. The major disadvantage of these biomarkers in the past has been the need to obtain CSF to measure them. However, the recent advances in extremely sensitive immunoassays made their measurement possible from peripheral blood even when present only in minuscule concentrations. This should mark the beginning of a new biomarker research and utilisation era in MS.

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“…N ON-CODING RNAS (ncRNAs) are RNA molecules that do not code for protein but nevertheless serve several functions in living cells, including the regulation of gene expression at all levels: transcription, splicing, and translation [1]. Naturally, they have been found to play important roles in diseases such as cancer [2], [3], [4] and multiple sclerosis [5], to name a few examples. Consequently, ncRNAs are also central to the development of novel and promising therapeutic approaches [6], [7], [8], [9], [10].…”

Section: Introductionmentioning

confidence: 99%

Assessing Global-Local Secondary Structure Fingerprints to Classify RNA Sequences With Deep Learning

Sutanto¹,

Turcotte²

2023

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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RNA elements that are transcribed but not translated into proteins are called non-coding RNAs (ncRNAs). They play wide-ranging roles in biological processes and disorders. Just like proteins, their structure is often intimately linked to their function. Many examples have been documented where structure is conserved across taxa despite sequence divergence. Thus, structure is often used to identify function. Specifically, the secondary structure is predicted and ncRNAs with similar structures are assumed to have same or similar functions. However, a strand of RNA can fold into multiple possible structures, and some strands even fold differently in vivo and in vitro. Furthermore, ncRNAs often function as RNA-protein complexes, which can affect structure. Because of these, we hypothesized using one structure per sequence may discard information, possibly resulting in poorer classification accuracy. Therefore, we propose using secondary structure fingerprints, comprising two categories: a higher-level representation derived from RNA-As-Graphs (RAG), and free energy fingerprints based on a curated repertoire of small structural motifs. The fingerprints take into account the difference between global and local structural matches. We also evaluated our deep learning architecture with k -mers. By combining our global-local fingerprints with 6-mer, we achieved an accuracy, precision, and recall of 91.04%, 91.10%, and 91.00%.

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A comprehensive review of non-coding RNAs functions in multiple sclerosis

Cited by 25 publications

References 36 publications

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: A Focus on Neurofilaments and Therapeutic Considerations

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: A Focus on Neurofilaments and Therapeutic Considerations

Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: a Comprehensive Review of the Literature with a Focus on Neurofilaments and Therapeutic Considerations

Assessing Global-Local Secondary Structure Fingerprints to Classify RNA Sequences With Deep Learning

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